private TemporaryDirectory ShareSkydFile(ZipFileShare zip, TemporaryDirectory tempDir)
{
string pathCache = ChromatogramCache.FinalPathForName(DocumentPath, null);
if (!File.Exists(pathCache))
{
return(tempDir);
}
if (ShareType.SkylineVersion != null && Document.Settings.HasResults)
{
var measuredResults = Document.Settings.MeasuredResults;
if (measuredResults.CacheVersion.HasValue &&
!measuredResults.CacheVersion.Equals(ShareType.SkylineVersion.CacheFormatVersion))
{
String cacheFileName = Path.GetFileName(pathCache);
if (cacheFileName != null)
{
if (tempDir == null)
{
tempDir = new TemporaryDirectory();
}
String newCachePath = Path.Combine(tempDir.DirPath, cacheFileName);
MinimizeToFile(newCachePath, CacheFormat.FromVersion(ShareType.SkylineVersion.CacheFormatVersion));
zip.AddFile(newCachePath);
return(tempDir);
}
}
}
zip.AddFile(pathCache);
return(tempDir);
}
private void ShareComplete(ZipFileShare zip)
{
TemporaryDirectory tempDir = null;
try
{
// If complete sharing, just zip up existing files
var pepSettings = Document.Settings.PeptideSettings;
var transitionSettings = Document.Settings.TransitionSettings;
if (Document.Settings.HasBackgroundProteome)
{
zip.AddFile(pepSettings.BackgroundProteome.BackgroundProteomeSpec.DatabasePath);
}
if (Document.Settings.HasRTCalcPersisted)
{
zip.AddFile(pepSettings.Prediction.RetentionTime.Calculator.PersistencePath);
}
if (Document.Settings.HasOptimizationLibraryPersisted)
{
zip.AddFile(transitionSettings.Prediction.OptimizedLibrary.PersistencePath);
}
if (Document.Settings.HasIonMobilityLibraryPersisted)
{
zip.AddFile(pepSettings.Prediction.IonMobilityPredictor.IonMobilityLibrary.PersistencePath);
}
var libfiles = new HashSet <string>();
foreach (var librarySpec in pepSettings.Libraries.LibrarySpecs)
{
if (libfiles.Add(librarySpec.FilePath))
// Sometimes the same .blib file is referred to by different library specs
{
zip.AddFile(librarySpec.FilePath);
if (Document.Settings.TransitionSettings.FullScan.IsEnabledMs)
{
// If there is a .redundant.blib file that corresponds
// to a .blib file, add that as well
IncludeRedundantBlib(librarySpec, zip, librarySpec.FilePath);
}
}
}
// ReSharper disable ExpressionIsAlwaysNull
tempDir = ShareDataAndView(zip, tempDir);
// ReSharper restore ExpressionIsAlwaysNull
if (null == ShareType.SkylineVersion)
{
zip.AddFile(DocumentPath); // CONSIDER(bpratt) there's no check to see if this is a current representation of the document - a dirty check would be good
}
else
{
tempDir = ShareDocument(zip, tempDir);
}
Save(zip);
}
finally
{
DeleteTempDir(tempDir);
}
}
private void Save(ZipFileShare zip)
{
CountEntries = zip.CountEntries;
using (var saver = new FileSaver(SharedPath))
{
zip.Save(saver.SafeName, SrmDocumentSharing_SaveProgress);
ProgressMonitor.UpdateProgress(_progressStatus.Complete());
saver.Commit();
}
}
private TemporaryDirectory ShareDataAndView(ZipFileShare zip, TemporaryDirectory tempDir)
{
tempDir = ShareSkydFile(zip, tempDir);
string viewPath = SkylineWindow.GetViewFile(DocumentPath);
if (File.Exists(viewPath))
{
zip.AddFile(viewPath);
}
return(tempDir);
}
private void IncludeRedundantBlib(LibrarySpec librarySpec, ZipFileShare zip, string blibPath)
{
if (librarySpec is BiblioSpecLiteSpec)
{
var redundantBlibPath = BiblioSpecLiteSpec.GetRedundantName(blibPath);
if (File.Exists(redundantBlibPath))
{
zip.AddFile(redundantBlibPath);
}
}
}
private void SafeAuditLog(ZipFileShare zip, string docPath)
{
if (ShouldShareAuditLog(Document, ShareType))
{
var path = SrmDocument.GetAuditLogPath(docPath);
if (File.Exists(path))
{
zip.AddFile(path);
}
}
}
private TemporaryDirectory ShareDocument(ZipFileShare zip, TemporaryDirectory tempDir, out string tempDocPath)
{
if (tempDir == null)
{
tempDir = new TemporaryDirectory();
}
string fileName = Path.GetFileName(DocumentPath) ?? string.Empty;
tempDocPath = Path.Combine(tempDir.DirPath, fileName);
Document.SerializeToFile(tempDocPath, tempDocPath,
ShareType.SkylineVersion ?? SkylineVersion.CURRENT, ProgressMonitor);
zip.AddFile(tempDocPath);
return(tempDir);
}
public void Share(IProgressMonitor progressMonitor)
{
ProgressMonitor = progressMonitor;
ProgressMonitor.UpdateProgress(_progressStatus = new ProgressStatus(DefaultMessage));
using (var zip = new ZipFileShare())
{
if (ShareType.Complete)
{
ShareComplete(zip);
}
else
{
ShareMinimal(zip);
}
}
}
private void ShareMinimal(ZipFileShare zip)
{
TemporaryDirectory tempDir = null;
try
{
var docOriginal = Document;
if (Document.Settings.HasBackgroundProteome)
{
// Remove any background proteome reference
Document = Document.ChangeSettings(Document.Settings.ChangePeptideSettings(
set => set.ChangeBackgroundProteome(BackgroundProteome.NONE)));
}
if (Document.Settings.HasRTCalcPersisted)
{
// Minimize any persistable retention time calculator
tempDir = new TemporaryDirectory();
string tempDbPath = Document.Settings.PeptideSettings.Prediction.RetentionTime
.Calculator.PersistMinimized(tempDir.DirPath, Document);
if (tempDbPath != null)
{
zip.AddFile(tempDbPath);
}
}
if (Document.Settings.HasOptimizationLibraryPersisted)
{
if (tempDir == null)
{
tempDir = new TemporaryDirectory();
}
string tempDbPath = Document.Settings.TransitionSettings.Prediction.OptimizedLibrary.PersistMinimized(
tempDir.DirPath, Document);
if (tempDbPath != null)
{
zip.AddFile(tempDbPath);
}
}
if (Document.Settings.HasIonMobilityLibraryPersisted)
{
// Minimize any persistable ion mobility predictor
if (tempDir == null)
{
tempDir = new TemporaryDirectory();
}
string tempDbPath = Document.Settings.TransitionSettings.IonMobilityFiltering.IonMobilityLibrary
.PersistMinimized(tempDir.DirPath, Document, null, out _);
if (tempDbPath != null)
{
zip.AddFile(tempDbPath);
}
}
if (Document.Settings.HasLibraries)
{
// Minimize all libraries in a temporary directory, and add them
if (tempDir == null)
{
tempDir = new TemporaryDirectory();
}
Document = BlibDb.MinimizeLibraries(Document, tempDir.DirPath,
Path.GetFileNameWithoutExtension(DocumentPath),
null,
ProgressMonitor);
if (ProgressMonitor != null && ProgressMonitor.IsCanceled)
{
return;
}
foreach (var librarySpec in Document.Settings.PeptideSettings.Libraries.LibrarySpecs)
{
var tempLibPath = Path.Combine(tempDir.DirPath, Path.GetFileName(librarySpec.FilePath) ?? string.Empty);
zip.AddFile(tempLibPath);
// If there is a .redundant.blib file that corresponds to a .blib file
// in the temp temporary directory, add that as well
IncludeRedundantBlib(librarySpec, zip, tempLibPath);
}
}
var auditLogDocPath = DocumentPath;
tempDir = ShareDataAndView(zip, tempDir);
if (ReferenceEquals(docOriginal, Document) && null == ShareType.SkylineVersion)
{
zip.AddFile(DocumentPath);
}
else
{
tempDir = ShareDocument(zip, tempDir, out auditLogDocPath);
}
SafeAuditLog(zip, auditLogDocPath);
Save(zip);
}
finally
{
DeleteTempDir(tempDir);
}
}
